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Question: Affy ClariomD human transcriptome annotation
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gravatar for anitabaery
6 months ago by
anitabaery0
anitabaery0 wrote:

Hi All,

I have annotated my data with

anno<- annotateEset(rma, pd.clariom.d.human)

however, I have noticed that there are ~6000 genes without chromosome and base positions assigned. I have checked and they do have position on NCBI (build37). Is it because the annotated file used for annotation is not updated? I have included some examples below.

Thank you Anita

 

PROBEID ENTREZID SYMBOL GENENAME CHR START END
TC0100006736.hg.1 102724539 LOC102724539 uncharacterized LOC102724539 NA NA NA
TC0100006804.hg.1 100847055 MIR5697 microRNA 5697 NA NA NA
TC0100006813.hg.1 100422970 MIR1273D microRNA 1273d NA NA NA
TC0100006815.hg.1 101954271 RNU6-9 RNA, U6 small nuclear 9 NA NA NA

         

 

 

 

 

 

 

ADD COMMENTlink modified 6 months ago by James W. MacDonald47k • written 6 months ago by anitabaery0
0
gravatar for James W. MacDonald
6 months ago by
United States
James W. MacDonald47k wrote:

The annotation packages we supply are simply a re-packaging of what we can download from affy, without having done any vetting on our part. So if they don't give the chromosome and position, we don't either. It wouldn't take much to add that information using the corresponding TxDb package.

ADD COMMENTlink written 6 months ago by James W. MacDonald47k
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